Special

MmuINT0085925 @ mm9

Intron Retention

Gene
ENSMUSG00000059022 | Kcp
Description
kielin/chordin-like protein [Source:MGI Symbol;Acc:MGI:2141640]
Coordinates
chr6:29432634-29434094:-
Coord C1 exon
chr6:29433930-29434094
Coord A exon
chr6:29432941-29433929
Coord C2 exon
chr6:29432634-29432940
Length
989 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TGATTGCTGTCTCCATGTAGGTC
3' ss Score
10.1
Exon sequences
Seq C1 exon
GTGCTGTGGGACGGGCAATCCCAGGTGGAGGTGAGAGTTCCCAGCTCCTACCGGGGCCAGACTTGTGGTCTCTGTGGGAACTTCAATGGCTTTGCCCAGGATGATCTGCAGGGTCCGGATGGGAGGCTCCTGCCCACAGAGGCTTCGTTTGGGAACAGCTGGAAG
Seq A exon
GTGAGTAGCTTGGGAGCAAGAAGTTGCAACAGGCTAAAGGAACTGGGTACAAGCCCCTGCTAGGGGACCCAAGACAGACTTCTGCATTGTCATGGAAGCTGGAGGTGTAAAAGCTTGCCTTGAAGAGGCAGATGGCCTGCTGGAAACCGTGTCACCTGAATCCCTAGAATGTGCTCTGTCACTCGCTGGCTGTGGAACCTTGAACAAGTTATTTACCTGTTTTAGCCTTAATTTATTTGTAAAAGGGAGACAAGATGAATATAGATGGTGCTTTTCTTTGCTGTCTTATTGATGTTGGTTTTGATATAGAATCTTGCTGGGTAGCCCATACCGGGCTCCAGCCTGATACCTTCTTATCCCAGCTTCCCGAGAACCAGGATCACACCTCAATGGGCACTTTCGCCTCTTTCTGTTTTGTTTTGAGACAGGGTCTCACATAACCCAGATCGTCCTATGTAGCCAGGAATAGCATTGAACGGCTGGTCCTCCTGCCTGTCTCCAAGTGCTGAGATTACAGGACTGCACCACTGTTTCCAGTTTTTTTATGCCACACAGAGTATCAAACAAAGGCAGGGCTTTGTGCTGTAGACAAGCAGTCTTCCGACTGTGCTGTTTCCACAGCCCAGTGTGTGCTGTTCTTGAGGGGACAGCTTTGATTCCTTTGCCTTTTCTTTTTTGACACAAAGTCTCGCCATGTTATCTAGATATTTCTAGCGCAGGATCCTCCTGCCCCAGGCTTCTAATGCTGGGATCATAGGTGTGTACCAGTATGCCTTGCCCTTAAAAATTAGCATATATTATTTATACATAATAATTTATTTCATTTTGATATTTTCATATATGTATATAATGTATTTTAGTCACCTTCCCAGCTAGCCCAAACCTCTACTTTCTTTAGTGGGGTGTAGTGGAGAGTTTATGGGAGCATCACAGGTCCTGCTCAATTTTGCCAGCCATGTTTCCACATCATGATTGCTGTCTCCATGTAG
Seq C2 exon
GTCCCCAAGGGGCTGGGGCCTGGCCGGCCGTGTTCTGCAGGCCGAGAGGTGGACCCGTGCCGGGCAGCAGGCTACCGTGCCAGGCGTGAGGCCAATGCCCGGTGCGGGATCCTGAAGACTTCACCGTTCAGTCATTGCCATGCTGTGGTGCCCCCGGAACCCTTCTTTGCTGCCTGTGTGTACGACTTGTGTGCTTGTGGTCCAGGCTCCTCCTCTGACACCTGTCTCTGTGATGCCCTTGAAGCCTACGCTAGCCACTGTCGCCAGGCAGGGGTGACTCCTGTCTGGAGGGGTCCTACACTCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059022-Kcp:NM_001029985:36
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.042 A=NA C2=0.005
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009420=VWD=PD(52.8=19.4),PF087426=C8=PU(97.4=51.4)

							
A:
NA

							
C2:
PF087426=C8=PU(97.4=71.8)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000099135





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000125076, ENSMUSP00000125076f5104A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:128877791-128878557 
ALTERNATIVE
HsaINT0084795
(KCP)
Human
(hg19)
chr7:128517845-128518611 
ALTERNATIVE
HsaINT0084795
(KCP)
Rat
(rn6)
chr4:56760910-56762161 
ALTERNATIVE
RnoINT0078155
(Kcp)
Cow
(bosTau6)
chr4:93656098-93656525 
LOW PSI
BtaINT0079964
(KCP)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGTGGAGGTGAGAGTTCCCAG

				
R: 
TGGACCACAAGCACACAAGTC

				
Band lengths: 
346-1335

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"